Duplicate, Duplicate Linked, or modifier?
A good Idea is to use a Particle system that uses the red object as sourc eobject.
If you do you could follow this steps:


create a plane
add the plane a particle system
set the start and end frame to 1 and the lifetime to an high number, for example 20000 (if you plan on doing an animation, the lifetime should be higher than the last frame number, so that the particle won't disappear)
Set emit from Faces, then Grid and set the resolution as high as you need.
Then set the red object as the source
in field weight settings, set the gravity to 0 so the particles won't just fall


in this way you can also create those little "valley" between the proteins (blue object) using a magnetic force field.